Quantum Chemical Calculations of NMR

Parameters
Tatyana Polenova
University of Delaware
Newark, DE

Winter School on Biomolecular NMR
January 20-25, 2008
Stowe, Vermont
OUTLI NE
INTRODUCTION
Relating NMR parameters to geometric and electronic structure
Classical calculations of EFG tensors
Molecular properties fromquantumchemical calculations
Quantumchemistry methods
DENSITY FUNCTIONAL THEORY FOR CALCULATIONS OF NMR PARMETERS
Introduction to DFT
Software
Practical examples
Tutorial
RELATI NG NMR OBSERVABLES TO
MOLECULAR STRUCTURE
NMR Spectrum NMR Parameters Local geometry


Chemical structure
(reactivity)
I. Calculation of experimental NMR parameters
Find unique solution to C
Q
,
Q
,

, , ,
II. Theoretical prediction of fine structure constants
from molecular geometry
Classical electrostatic model (EFG)- only in simple ionic compounds
Quantum mechanical calculations (Density Functional Theory) (EFG, CSA)
ELECTRI C FI ELD GRADI ENT (EFG) TENSOR:
POI NT CHARGE MODEL
EFG TENSOR IS DETERMINED BY THE COMBINED ELECTRONIC AND NUCLEAR
WAVEFUNCTION, NO ANALYTICAL EXPRESSION IN THE GENERL CASE
THE SIMPLEST APPROXIMATION: CLASSICAL POINT CHARGE MODEL
ATOMS CONTRIBUTING TO THE EFG TENSOR ARE TREATED AS POINT CHARGES,
THE RESULTING EFG TENSOR IS THE SUM WITH RESPECT TO ALL ATOMS
VERY CRUDE MODEL, WORKS QUANTITATIVELY ONLY IN SIMPLEST IONIC
SYSTEMS, BUT YIELDS QUALITATIVE TRENDS AND GENERL UNDERSTANDING
OF THE SYMMETRY AND MAGNITUDE OF THE EXPECTED TENSOR
V
2,k
=
Z
i
e
d
i
3
i=1
n

4
5
Y
2,k

i
,
i
( )
ELECTRI C FI ELD GRADI ENT (EFG) TENSOR:
POI NT CHARGE MODEL
V
2,k
=
Z
i
e
d
i
3
i=1
n

4
5
Y
2,k

i
,
i
( )
V
2,0
=
Ze
d
3
; V
2,1
= 0; V
2,2
= 0
V
2,0
=
2Ze
d
3
; V
2,1
= 0; V
2,2
= 0
V
2,0
=
3
2
Ze
d
3
; V
2,1
= 0; V
2,2
= 0
V
2,0
= 0; V
2,1
= 0; V
2,2
= 0
MOLECULAR PROPERTI ES FROM QUANTUM
CHEMI CAL CALCULATI ONS
H = E
See for example M. Head-Gordon (1996) J. Phys. Chem. 100, 13213-13225
QUANTUM CHEMI STRY METHODS
SEMI-EMPIRICAL METHODS
Based on Hartree-Fock approach. A Fock matrix is constructed, and the Hartree-Fock
equations are iteratively solved. The approximations are in the construction of the Fock
matrix (the energy expressions) and are based upon empirical data.
AB INITIO METHODS
Make no use of empirical information, except for the fundamental constants of nature,
such as the mass of the electron, Plancks constant, etc.
Do not confuse ab initio with exact!
DENSITY FUNCTIONAL THEORY METHODS
Include the electron correlation, which is introduced by adapting the expression for the
density of a uniformelectron gas to the molecular orbital environment. Replace the
many-body electronic wavefunction with the electronic density as the basic quantity.
H = E
Schrdinger equation- cannot be solved exactly for multi-electron systems,
and approximations have to be made
USEFUL DEFI NI TI ONS
AO (ATOMIC ORBITAL)
An orbital described by a wavefunction for a single electron centered on a single atom.
ORBITAL
The wavefunction describing where an electron is within an atomor a molecule.
BASIS SET
Finite set of functions used to approximately express the molecular orbital (MO)
wavefunction(s) of a system, normally atomcentered, consisting of AOs differing in local
angular momentumfor each atom. The basis set can be interpreted as restricting each
electron to a particular region of space.
ELECTRON CORRELATION
Explicitly considering the effect of the interactions of specific electron pairs, rather than
the effect that each electron feels fromthe average of all the other electrons.
GAUSSIANS
Functions frequently used as primitive functions to expand the total wavefunction.
USEFUL DEFI NI TI ONS
GIAO (GAUGE INDEPENDENT ATOMIC ORBITALS)
Ditchfield's method for canceling out the arbitrariness of the choice of origin & form
(gauge) of the vector potential used to introduce the magnetic field in the Hamiltonian
when calculating chemical shielding and chemical shift tensor. An exponential term
containing the vector potential is included with each atomic orbital. Originally developed
based on Hartree-Fock, improved by Pulay w/ DFT to be faster, also used w/MP2 & CCSD.
Pros: less basis set dependence than IGAIM.
FOR MORE DEFINITIONS, SEE
http://www.chamotlabs.com/Freebies/Acronyms.html
SEMI -EMPI RI CAL METHODS
LIMITED TO HUNDREDS OF ATOMS
MNDO, AM1, PM3
Were designed to reproduce heats of formation and structures of a large number of
organic molecules
INDO/S, CNDO/S
Good at prediction of electronic transitions in the UV/VIS spectral region
AB I NI TI O METHODS
LIMITED TO TENS OF ATOMS
GIVE THE ABSOLUTE ENERGY OF THE SYSTEM OF FIXED NUCLEI AND
MOVING ELECTRONS
One of the most useful features of the ab initio MO theory is that it allows the definition of
model chemistries. A theoretical model chemistry entails a method (e.g., Hartree-Fock
or MP2 etc.) and a basis set. The philosophy of a model chemistry is that it should be
uniformly applicable and tested on as many systems as possible to learn about its
performance.
DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
INCLUDE THE ELECTRON CORRELATION
Electron correlation is introduced by adapting the expression for the density of a uniform
electron gas to the molecular orbital environment.
Replace the many-body electronic wavefunction with the electronic density as the basic
quantity. Many-body wavefunctions- dependent on 3N variables (3 spatial variables for
each of the N electrons), the density- dependent on 3 spatial variables.
http://en.wikipedia.org/wiki/Density_functional_theory
DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
MOST COMMON IMPLEMENTATION- KOHN-SHAM METHOD
The intractable many-body problemof interacting electrons in a static external potential
is reduced to a tractable problemof non-interacting electrons moving in an effective
potential.
Effective potential- includes the external potential and the effects of the Coulomb
interactions between the electrons, e.g. the exchange and correlation interactions.
To model the latter, the local-denisty approximation (LDA) is used, which is based upon
exact exchange energy for a uniformelectron gas (obtained fromthe Thomas-Fermi
model), and fromfits to the correlation energy for a uniformelectron gas.
http://en.wikipedia.org/wiki/Density_functional_theory
DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
MANY-ELECTRON SCHRDINGER EQUATION:
U- interaction termfor many-particle problem
Approaches: expansion of wave function in Slater determinants (HF and post-HF
metthods)
Problem: computationally expensive, impractical in large systems
http://en.wikipedia.org/wiki/Density_functional_theory
H+= T +V +U
[ ]
+= ~
h
2
2m
V
i
2
~
i
N
_
V
r
r
i
( )
i
N
_
+ U
r
r
i
,
r
r
j
( )
i< j
_
|
|
|
|
|
|
|
|
+= E+
DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
DFT ALTERNATIVE:
Introduce a newvariable, the particle density
Hohenberg and Kohn- proved (1964) that the expression is unique, i.e. to a given ground
state density n
0
(r) it is possible to calculate the corresponding ground state wavefunction

0
is a unique functional of n
0
, i. e.

0
=
0
[n
0
]
Therefore, all other ground state observables (including energy) are also functionals of n
0
<O>[n
0
] =<
0
[n
0
]|O|
0
[n
0
]>
E
0
=E[n
0
] =<
0
[n
0
]|T+V+U|
0
[n
0
]>
where the contribution of the external potential <
0
[n
0
]|U|
0
[n
0
]>can be written
explicitly in terms of the density
http://en.wikipedia.org/wiki/Density_functional_theory
n
r
r
( )
= N d
3
r
2

d
3
r
2
...

d
3
r
N

*
r
r
1
,
r
r
2
,...,
r
r
N
( )

r
r
1
,
r
r
2
,...,
r
r
N
( )

0
r
r
1
,
r
r
2
,...,
r
r
N
( )
V n
[ ]
= V
r
r
( )
n

r
r
( )
d
3
r
DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
For a particular systemwith V specified, minimize the functional
with respect to n(r), assuming reliable expressions are known for T[n] and U[n]. Successful
minimization- yields ground state density n
0
and thus all other ground-state observables.
Minimization of energy functional E[n] - by Lagrangian method of undetermined multipliers.
Rewrite the functional as a fictitious density functional of a non-interacting system
E
s
[n] =<
s
[n]|T
s
+V
s
|
s
[n]>
T
s
-non-interacting kinetic energy, V
s
- external effective potential in which particles are moving
Then solve Kohn-Shamequations of this auxillary non-interacting system
Which yields the orbitals
i
that reproduce the density n(r) of the original many-body system
http://en.wikipedia.org/wiki/Density_functional_theory
E n
[ ]
= T n
[ ]
+U n
[ ]
+ V
r
r
( )
n

r
r
( )
d
3
r
~
h
2
2m
V
2
+V
s
r
r
i
( )
|
|
|
|
|
|

i
r
r
( )
= r
i

i
r
r
( )

n
r
r
( )
=
def
n
s
r
r
( )
=
i
r
r
( )
2
i
N

DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
EFFECTIVE SINGLE-PARTICLE POTENTIAL CAN BE WRITEN AS
Hartree term(describes the electron-electron Coulomb repulsion)
V
XC
- Exchange correlation potential, includes all the many-particle
interactions
Since the Hartree termand V
XC
depend on n(r), which depends on the orbitals
i
, which in turn
depend on V
S
, the problemof solving the Kohn-Shamequations has to be done in a self-
consistent (iterative) way. Start with an initial guess of n(r), then calculate the corresponding
V
S
and solve the Kohn-Shamequations for
i
. Fromthese calculate a newdensity and start
again, repeat until convergence is reached.
http://en.wikipedia.org/wiki/Density_functional_theory
V
s
=V +
e
2
n
s
r
r
( )
r
r
r
r
d
3
r +V
XC
n
r
r
( ) [ ]

e
2
n
s
r
r
( )
r
r
r
r
d
3
r

DENSI TY FUNCTI ONAL THEORY (DFT)
METHODS
APPROXIMATIONS
Problem: exact functionals for exchange and correlation are not known except for the free
electron gas. Approximations are needed.
Local-density approximation (LDA)- the functional depends only on the density at the
coordinate where the functional is evaluated:
Local spin-density approximation (LSDA)- generalization of LDA to include electron spin:
Generalized gradient approximations (GGA)- take into account the gradient of the density at the
same coordinate:
GGA- yields very good results for molecular geometries and ground state energies.
http://en.wikipedia.org/wiki/Density_functional_theory
E
XC
n
[ ]
=
XC
n
( )
n r
( )
d
3
r

E
XC
n

, n

[ ]
=
XC
n

, n

( )
n r
( )
d
3
r

E
XC
n

, n

[ ]
=
XC
n

, n

,
r
n

,
r
n
( )
n r
( )
d
3
r

BASI S SETS
THE SET OF ONE-ELECTRON WAVEFUNCTIONS USED TO BUILD MOLECULAR
ORBITAL WAVEFUNCTIONS
Examples of Gaussian basis sets:
STO-3G, 3-21G (H-Xe), 6-31G (H-Cl), 6-311G (H-Kr);
6-31G (d); 6-31G (d,p); 6-31+G (d,p); 6-311+G (3df,2p);
Aug-cc-pVTZ;
Effective core potentials: LANL2MB (H-Ba, La-Bi); LANDZ; SDD- entire Periodic
Table
And many more basis sets tailored to specific systems
Useful basis set depository- EMSL basis set exchange:
http://gnode2.pnl.gov/bse/portal
http://www.gaussian.com/00000485.htm
DENSI TY FUNCTI ONAL THEORY (DFT):
SOFTWARE
http://en.wikipedia.org/wiki/Density_functional_theory
Abinit GAUSSIAN SPR-KKR
ADF GPAW TURBOMOLE
AIMPRO JAGUAR (no EFG) VASP
Atomistix Toolkit MOLPRO WIEN2k (no CSA)
Atompaw/PWPAW NRMOL
CADPAC NWChem
CASTEP (NMR CASTEP) OCTOPUS
CPMD OpenMX
CRYSTAL06 ORCA
DACAPO ParaGauss
DALTON PARATEC
deMon2K PARSEC
DFT++ PCGAMESS
DMol3 PLATO
EXCITING Parallel QuantumSolutions
Fireball Priroda
FLEUR Q-Chem
Fsatom SIESTA
GAMESS (UK) Socorro
GAMESS (US) S/PHI/nX
RECALL THE BASIC DEFINITIONS FOR EFG TENSOR:
Electric field (vector property):
where is the electrostatic potential:
Electric field gradient:
(tensor of rank 2)
Quadrupolar coupling constant:
DENSI TY FUNCTI ONAL THEORY:
ELECTRI C FI ELD GRADI ENT TENSOR
E =
V = E
C
Q
=
V
ZZ
eQ ( )
h
, Qelectric quadrupole moment

1
=

2
dV
2
4
0
r
12

RECALL THE DEFINITION OF THE MAGNETIC SHIELDING ANISOTROPY TENSOR:
where is the nuclear magnetic moment, and B is an external magnetic field.
Early chemical shift calculations: C. Jameson, A. DeDios, E. Oldfield
DENSI TY FUNCTI ONAL THEORY:
MAGNETI C SHI ELDI NG TENSOR

i, j
=

2
E

i
B
j

DEVELOPED BY THE GROUP OF J. A. POPLE
USES GAUSSIAN BASIS SETS
ONE OF THE MOST USER-FRIENDLY PROGRMS FOR RUNNING ELECTRONIC
STRUCTURE CALCULATIONS
CAPABILITIES RELEVANT TO NMR SPECTROSCOPISTS:
Geometry optimization
Calculations of EFG tensors
Calculations of magnetic shielding anisotropy tensors
Calculations of spin-spin coupling constants
TYPES OF CALCULATIONS:
Semi-empirical
Ab initio
DFT
Hybrid QM/MM
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
GAUSSIAN CAN RUN MANY TYPES OF CALCULATIONS, AND THE USER
SELECTS WHICH BY GIVING A SERIES OF KEYWORDS, WHICH REPRESENT
THE DESIRED TYPE OF CALCULATION. EACH OF THE KEYWORDS USUALLY
HAS A NUMBER OF OPTIONS, SPECIFIED IN THE FORM
KEYWORD=(OPTION1,OPTION2,OPTION3)
The ordering of keywords and options is not important, and lower and upper case characters
are treated equal.
Gaussian reads the keywords and other information (e.g., geometry) froman input file, which
must have a name of the type
jobname.com
To run the program, type
g03 jobname.com&
which produces an output file called jobname.log
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
EXAMPLE:
---
%chk=formald.chk
%nproc=2
%mem=120MB
#B3LYP/6-31G(d) opt NMR EFG
Formaldehyde optimization
0 1 multiplicity
C 0.0 0. 0 0.0
O 0.0 1.22 0.0
H 0.94 -0.54 0.0
H -0.94 -0.54 0.0
Charge
Title
Cartesian
Coordinates
or Z-matrix
THE BASIC STRUCTURE OF A
GAUSSIAN INPUT:
Link 0 Commands:
Locate and name scratch files.
2 processors
Memory allocation - 120 MB
Route section (#lines): Specify desired
calculation type, (blank line terminated).
Title section
(blank line terminated).
Molecule specification
(blank line terminated).
Optional additional sections
(usually blank line terminated).
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
THE ROUTE SECTION OF A GAUSSIAN03 INPUT FILE SPECIFIES
THE TYPE OF CALCULATION TO BE PERFORMED. THERE ARE
THREE KEY COMPONENTS TO THIS SPECIFICATION:
The job type
(OPT, FREQ, NMR, PROP=EFG)
http://www.gaussian.com/g_ur/m_jobtypes.htm
The method
(HF, AM1, B3LYP, CASSCF)
The basis set
(3-21G, 6-31G(d),6-311+G(d,p), cc-pVTZ, etc.)
http://www.gaussian.com/g_ur/m_basis_sets.htm
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
The first line of the molecule specification section specifies the net electric charge (a
signed integer) and the spin multiplicity (a positive integer).
Thus, for a neutral molecule in a singlet state, the entry 0 1 is appropriate.
For a radical anion, -1 2 would be used.
This is the only molecule specification input required if Geom=Check is used.
The entire molecule specification (and title section) may be omitted
by including Geom=AllCheck in the route section.
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
SAMPLE INPUT FILE FOR CALCULATING
51
V CSA AND EFG TENSORS FOR
VOCl
3
%nproc=1
%mem=700MB
%Chk=./VOCl3_opt_6311Gdp.chk
#b3lyp/6-311+G(d,p) opt=(maxcycle=100) scf=(vshift=100,maxcycle=256)
VOCl3
0 1
V -0.000056 -0.000022 0.230882
O -0.000052 -0.000075 1.803662
Cl 1.215304 -1.787943 -0.387058
Cl -2.156194 -0.158336 -0.387084
Cl 0.940990 1.946345 -0.387011
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
SAMPLE OUTPUT FILE FOR CALCULATING
51
V CSA AND EFG TENSORS FOR
VOCl
3
(CSA ENTRIES)
Calculating GIAO nuclear magnetic shielding tensors.
SCF GIAO Magnetic shielding tensor (ppm):
1 V Isotropic =-2279.3913 Anisotropy = 369.7210
XX=-2032.9731 YX= -0.0448 ZX= -0.0097
XY= -0.0404 YY=-2032.9397 ZY= -0.0515
XZ= 0.0107 YZ= -0.1385 ZZ=-2772.2612
Eigenvalues: -2772.2612 -2033.0021 -2032.9106
2 O Isotropic =-1148.8385 Anisotropy = 1752.5744
XX=-1732.9364 YX= -0.0137 ZX= -0.0339
XY= -0.0159 YY=-1733.1237 ZY= 0.0761
XZ= -0.0323 YZ= 0.0549 ZZ= 19.5444
Eigenvalues: -1733.1248 -1732.9352 19.5444
3 Cl Isotropic = -51.5475 Anisotropy = 998.2683
XX= 376.6950 YX= -34.6272 ZX= -476.2807
XY= -34.6678 YY= 340.4831 ZY= 286.9402
XZ= -494.8562 YZ= 298.1174 ZZ= -871.8206
Eigenvalues: -1088.1035 319.4962 613.9647
4 Cl Isotropic = -51.5914 Anisotropy = 998.3747
XX= 379.3590 YX= 33.0426 ZX= 487.1986
XY= 33.1260 YY= 337.8399 ZY= 268.1242
XZ= 506.2733 YZ= 278.5711 ZZ= -871.9731
Eigenvalues: -1088.3077 319.5417 613.9917
5 Cl Isotropic = -52.0678 Anisotropy = 998.7335
XX= 318.8621 YX= 1.5137 ZX= -11.0368
XY= 1.4978 YY= 397.5075 ZY= -556.1673
XZ= -11.4555 YZ= -577.4015 ZZ= -872.5730
Eigenvalues: -1088.7912 318.8333 613.7545
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
SAMPLE OUTPUT FILE FOR CALCULATING
51
V CSA AND EFG TENSORS FOR
VOCl
3
(EFG ENTRIES)
-----------------------------------------------------------------
Center ---- Electric Field Gradient ----
XX YY ZZ
-----------------------------------------------------------------
1 Atom -33460.854654 -33460.854707 -33459.870669
2 Atom -1241.359443 -1241.359442 -1241.173551
3 Atom -13077.544551 -13077.182276 -13076.272504
4 Atom -13077.571052 -13077.155932 -13076.272663
5 Atom -13076.975620 -13077.751573 -13076.272758
-----------------------------------------------------------------
-----------------------------------------------------------------
Center ---- Electric Field Gradient ----
XY XZ YZ
-----------------------------------------------------------------
1 Atom -0.000012 -0.000023 0.000045
2 Atom 0.000001 -0.000002 0.000087
3 Atom 0.344135 0.652327 -0.394042
4 Atom -0.328898 -0.667307 -0.368130
5 Atom -0.015211 0.014992 0.761941
-----------------------------------------------------------------
-----------------------------------------------------------------
Center ---- Electric Field Gradient ----
---- Eigenvalues ----
-----------------------------------------------------------------
1 Atom -33460.854709 -33460.854651 -33459.870669
2 Atom -1241.359444 -1241.359441 -1241.173551
3 Atom -13078.074600 -13076.974518 -13075.950213
4 Atom -13078.074716 -13076.974577 -13075.950354
5 Atom -13078.074258 -13076.975322 -13075.950371
-----------------------------------------------------------------
CALULATI NG NMR PARAMETERS I N
GAUSSI AN03
SAMPLE OUTPUT FILE FOR CALCULATING
51
V CSA AND EFG TENSORS FOR
VOCl
3
(EFG ENTRIES)
-----------------------------------------------------------------
Center ---- Electric Field Gradient ----
( tensor representation )
3XX-RR 3YY-RR 3ZZ-RR
-----------------------------------------------------------------
1 Atom -0.327977 -0.328030 0.656008
2 Atom -0.061964 -0.061963 0.123928
3 Atom -0.544774 -0.182499 0.727273
4 Atom -0.571170 -0.156050 0.727220
5 Atom 0.024364 -0.751590 0.727226
-----------------------------------------------------------------
-----------------------------------------------------------------
Center ---- Electric Field Gradient ----
( tensor representation )
---- Eigenvalues ----
-----------------------------------------------------------------
1 Atom -0.328033 -0.327975 0.656008
2 Atom -0.061965 -0.061962 0.123928
3 Atom -1.074823 0.025259 1.049564
4 Atom -1.074834 0.025306 1.049528
5 Atom -1.074274 0.024662 1.049612
-----------------------------------------------------------------
VI SUALI ZI NG THE RESULTS OF NMR
PARAMETER CALCULATI ONS I N GAUSSI AN03
GAUSSVIEW CAN GRPHICALLY DISPLAY A VARIETY OF GAUSSIAN
CALCULATION RESULTS, INCLUDING THE FOLLOWING:
Optimized molecular structures
Molecular orbitals
Atomic charges
Electron density surfaces fromany computed density
Electrostatic potential surfaces
NMR shielding density
Animation of the normal modes corresponding to vibrational frequencies
http://www.hoffmann-oberhausen.de/gvbroc.htm
CONVERTI NG GAUSSI AN03 RESULTS TO
STANDARD NMR NOTATI ON
MATHEMATICA ROUTINE GAUSSIAN
Reads every Gaussian output file in a specified directory
Searches for CSA and EFG tensor entries for V (can be modified for any nucleus)
Outputs EFG tensor (C
Q
in MHz) and
Q
and CSA tensor (

in ppmand

)
Outputs a summary table with the NMR tensors and the Euler angles
Available fromTatyana Polenova upon request
DFT CALCULATI ONS OF NMR PARAMETERS
FOR METALS: PRACTI CAL CONSI DERATI ONS
INCLUDING COUNTER IONS AND GENERLLY CHARGES OUTSIDE OF THE
IMMEDIATE COORDINATION SPHERE IS NECESSARY
Experiment
Simulation
S. Bolte, K. J. Ooms, B. Baruah, J. Smee, D. Crans, T. Polenova (2008) J.Chem. Phys.
DFT CALCULATI ONS CAN EXPLAI N THE
MAGNI TUDE OF C
Q
51
V SPECTROSCOPY OF DIPICOLINIC
ACID DERIVATIVES
Nominal coordination geometry:
heptacoordinate, large C
Q
expected
Experimental C
Q
: 3.43 MHz (small)
Electrostatic potential surface (ESP):
Reveals capped square planar charge
distribution, consistent with small C
Q
Ooms, Bolte, Baruah, Smee, Crans, Polenova (2007) Inorg. Chem. 46, 9285-9293
DFT ANALYSI S OF MOLECULAR ORBI TALS
51
V SPECTROSCOPY OF DIPICOLINIC
ACID DERIVATIVES
EXAMINE THE SYMMETRY OF MOS
USING THE NCS METHOD TO
UNDERSTAND THE CONTRIBUTIONS OF
CHEMICAL BONDS AND LONE ELECTRON
PAIRS TO THE
51
V MAGNETIC
SHIELDING TENSOR
Bolte, Ooms, Baruah, Smee, Crans, Polenova (2008) J.Chem. Phys.
DFT CALCULATI ONS OF NMR PARAMETERS
FOR METALS: PRACTI CAL CONSI DERATI ONS
ACCURCY OF EXPERIMENTALLY MEASURED EFG TENSORS
5-15% for small molecules
10-30% for proteins
BASIS SET
Compromise between the desired accuracy and the size of the system
For heavier elements- need custombasis sets with additional functions for core
electrons (to account for non-spherical charge distribution)
Check for the basis set convergence on small model systems first
METHOD
Choice of functional and basis set-
check on small model systems first
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
1. CREATE A DIRECTORY ON CRUNCH (4-PROCESSOR LINUX AMD OPTERON
WORKSTATION IN T. POLENOVAS LABORTORY) YOU WILL NEED AN X11
APPLICATION (MAC) OR USE PUTY
The login and password are available fromTatyana Polenova upon request;
Once on crunch,
$ mkdir yourlastname # this will make a directory for you
$ cp -r VOCl3/*.com yourlastname #copy the Gaussian executable .comfiles in VOCl3
directory to your directory
$ ls VOCl3 #list the contents of the VOCl3 directory; you
should see a number of files (.com, .log, .chk, and
.xyz) representing the input, output, checkpoint,
and coordinate files for the Gaussian jobs in this
tutorial
$ cd yourlastname #change directory to your directory
$ ls # list the contents; you should see two entries:
VOCl3_NMR_afteropt_Zampella.com, VOCl3_opt_b3lyp.com
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
2. EXAMINE THE CONTENTS OF YOUR GAUSSIAN INPUT FILES
$ more VOCl3_opt_6311Gdp.com #to see the VOCl3_opt_6311Gdp.comfile
$ more VOCl3_NMR_afteropt_b3lyp.com #to see the VOCl3_NMR_afteropt_b3lyp.comfile
Questions:
1. What type of jobs each of the two input files is written for?
2. What DFT method is used?
3. What basis sets are used?
4. Identify the coordinate entries
5. List the molecular parameters that are calculated in each file
6. In your spare time, identify other keywords that are used in the two files (consult Gaussian03
manual)
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
3. RUN GEOMETRY OPTIMIZATION ON THE VOCl
3
MOLECULE
$ setGauss #set Gaussian03 environment variables
$ nohup g03 VOCl3_opt_Zampella.com& #executes VOCl3_opt_Zampella.comin Gaussian03
Note that the job uses a custombasis set:
On vanadium- a LanL2DZ modified by Couty and Hall (Couty and Hall, J. Comput. Chem. 1996, 17,
1359-1370) and used by Zampella et al. for calculations of QMmodels of VCPO (Zampella et al.,
Inorg. Chem. 2004, 43, 4127-4136), and to make the geometry optimization quicker
This job will take approximately 4-15 minutes (depending on howmany jobs are running
simultaneously on crunch)
After this job is done, examine the corresponding log file. The coordinates for the optimized
geometry will be given in the last Input Orientation and Standard Orientation entries of the file.
To check whether the job is running, type top at any stage. Gaussian job names start with l
followed by 3 or 4 numbers, e.g. l703.exe, l502.exe, l1110.exe, etc. (read Gaussian manual for
more information). To exit top, type q.
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
5. CALCULATE THE EFG AND CSA TENSORS FOR THE GEOMETRY-OPTIMIZED
VOCl
3
$ g03 VOCl3_NMR_afteropt_b3lyp.com& #executes VOCl3_NMR_afteropt_b3lyp.comin
Gaussian03
This job will take approximately 20-45 minutes depending on the howmany jobs are running in
parallel
This job will calculate the EFG and CSA tensors on the geometry-optimized VOCl
3
molecule, and
performthe NCS (Natural Chemical Shielding) analysis to determine the contributions of the
individual bonds and lone electron pairs to the shift.
After the job is done, examine the contents of the corresponding log file. The CSA tensors will be
printed for each atom; the EFG tensors will be given as well (in atomic units).
Note that the 6-311+G(d,p) basis set is used, and the starting geometry is that optimized for a VOCl
3
job at the same level of theory (which we will not do because it takes 33 min, so I have run the
optimization in advance)
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
6. EXAMINE THE RESULTS OF GEOMETRY OPTIMIZATION IN MOLDEN
Molden- a free visualization program for displaying molecular structures; reads of Gaussian
input and output fles, and an easy analysis of geometry and SCF convergence
http://www.cmbi.ru.nl/molden/molden.html;
http://www.cmbi.ru.nl/molden/howtoget.html
$ molden & #executes Molden
Fromthe Molden Control menu, read VOCl3_opt_Zampella.log;
Select DrawMode: Solid/Ball-and-Stick
(ignore the error message about being unable
to read the basis set- this is irrelevant)
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
6. EXAMINE THE RESULTS OF GEOMETRY OPTIMIZATION IN MOLDEN (COND)
Examine the geometry convergence by selecting:
Convergence/Geom. Conv.
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
6. EXAMINE THE RESULTS OF GEOMETRY OPTIMIZATION IN MOLDEN (COND)
Click on each of the points along the plot; the corresponding geometry will be displayed in the molecule window
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
6. EXAMINE THE RESULTS OF GEOMETRY OPTIMIZATION IN MOLDEN (COND)
You can save the geometry produced at any step of the optimization:
Select Write/XYZ (or any other coordinate file that is supported by the program)
Note that you can then directly paste the coordinates produced by saving the XYZ file
into the input file for the single point calculations of the NMR parameters that you will
be executing subsequently
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. EXAMINE THE RESULTS OF NMR PARMETER CALCULATIONS USING
GAUSSVIEW
$ gview #executes GaussView
In GaussView, open the checkpoint file VOCl_NMR_afteropt_b3lyp.chk
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. EXAMINE THE RESULTS OF NMR PARMETER CALCULATIONS USING
GAUSSVIEW: ESP SURFACE
After opening the checkpoint file, go to Results/Surfaces; under cube actions, select NewCube; Kind: Total
Density, leave all the settings at default
It will take a minute or so for the programto generate the cube; then a line of data will appear under Cubes
Available
Under Cube Actions, select NewCube/Kind: ESP, leave all the settings as defaults
It will take a fewminutes to generate the ESP cube; then a line of data will also appear under Cubes Available
Next, select an appropriate isosurface value (0.0002 is appropriate for this example); generally adjust the
isosurface value until the visualization if the difference densities is ideal
For more details, see: http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. EXAMINE THE RESULTS OF NMR PARMETER CALCULATIONS USING
GAUSSVIEW: ESP SURFACE (COND)
Under Cubes Available, select Electron Density fromTotal SCF Density
Select Surface Actions; NewMapped Surface
Under Surface Mapping window, select Use an Existing Cube
Under Cubes Available, select Electrostatic Potential fromTotal SCF Density; click OK
A line of data will appear under Surfaces Available;
The mapped ESP surface will be displayed in the graphical window
For more details, see: http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. EXAMINE THE RESULTS OF NMR PARMETER CALCULATIONS USING
GAUSSVIEW: ESP SURFACE (COND)
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. EXAMINE THE RESULTS OF NMR PARMETER CALCULATIONS USING
GAUSSVIEW: ESP SURFACE (COND)
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. VISUALIZE MOLECULAR ORBITALS IN GAUSSVIEW
Open the checkpoint file
VOCl3_NMR_afteropt_b3lyp.chk
in GaussView;
Go to the Orbital Editor
On the right side,
orbitals are listed
Under Diagram, you can
arrange those with respect to
Energy or occupancy
For more details, see: http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. VISUALIZE MOLECULAR ORBITALS IN GAUSSVIEW
Under Visualize, select the set of orbitals
you would like to display (e.g., LUMO)
Keep the settings as default
For more details, see: http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm
PRACTI CAL EXERCI SE: CALCULATI ON OF
NMR PARAMETERS AND MOLECULAR
ORBI TALS FOR VOCl3
7. VISUALIZE MOLECULAR ORBITALS IN GAUSSVIEW
To display another orbital, select it in the menu on
The right side and click Update
For more details, see: http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm
SOME LI TERATURE
E. Oldfield QuantumChemical Studies of Protein Structure Phil. Trans. R. Soc. B 360: 1347-1361 (2005)
M. Head-Godron QuantumChemistry and Molecular Processes J. Phys. Chem. 100: 13213-13225 (1996)